I'm worried that the only ones seem to be email and the web, both of which came into existence when the internet was small and academic and it was natural for universities to decentralize. And running email on your own is getting increasingly hard because of spam and IP reputation. (We seem to have more-or-less won the war on spam, but at the cost of making email much less decentralized than it used to be.)
There's a mention of BitTorrent elsewhere in these comments, and there might be an argument for Bitcoin. But even for IRC, people tend not to run their own servers (although they could); there are a very small number of IRC networks, run by random people.
I would love to see a decentralized and federated team chat app along the lines of Slack or Discord, but I'm having trouble believing that such a thing would have a chance of success in a post-1995 internet.